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# Copyright 2000-2003 Jeff Chang.
# Copyright 2001-2008 Brad Chapman.
# Copyright 2005-2012 by Peter Cock.
# Copyright 2006-2009 Michiel de Hoon.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Represent a Sequence Feature holding info about a part of a sequence.
This is heavily modeled after the Biocorba SeqFeature objects, and
may be pretty biased towards GenBank stuff since I'm writing it
for the GenBank parser output...
What's here:
Base class to hold a Feature.
----------------------------
classes:
o SeqFeature
Hold information about a Reference.
----------------------------------
This is an attempt to create a General class to hold Reference type
information.
classes:
o Reference
Specify locations of a feature on a Sequence.
---------------------------------------------
This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in
much the same way as Biocorba. This has the advantages of allowing us
to handle fuzzy stuff in case anyone needs it, and also be compatible
with Biocorba.
classes:
o FeatureLocation - Specify the start and end location of a feature.
o ExactPosition - Specify the position as being exact.
o WithinPosition - Specify a position occuring within some range.
o BetweenPosition - Specify a position occuring between a range (OBSOLETE?).
o BeforePosition - Specify the position as being found before some base.
o AfterPosition - Specify the position as being found after some base.
o OneOfPosition - Specify a position where the location can be multiple positions.
o UnknownPosition - Represents missing information like '?' in UniProt.
"""
from Bio.Seq import MutableSeq, reverse_complement
class SeqFeature(object):
"""Represent a Sequence Feature on an object.
Attributes:
o location - the location of the feature on the sequence (FeatureLocation)
o type - the specified type of the feature (ie. CDS, exon, repeat...)
o location_operator - a string specifying how this SeqFeature may
be related to others. For example, in the example GenBank feature
shown below, the location_operator would be "join"
o strand - A value specifying on which strand (of a DNA sequence, for
instance) the feature deals with. 1 indicates the plus strand, -1
indicates the minus strand, 0 indicates stranded but unknown (? in GFF3),
while the default of None indicates that strand doesn't apply (dot in GFF3,
e.g. features on proteins). Note this is a shortcut for accessing the
strand property of the feature's location.
o id - A string identifier for the feature.
o ref - A reference to another sequence. This could be an accession
number for some different sequence. Note this is a shortcut for the
reference property of the feature's location.
o ref_db - A different database for the reference accession number.
Note this is a shortcut for the reference property of the location
o qualifiers - A dictionary of qualifiers on the feature. These are
analagous to the qualifiers from a GenBank feature table. The keys of
the dictionary are qualifier names, the values are the qualifier
values.
o sub_features - Additional SeqFeatures which fall under this 'parent'
feature. For instance, if we having something like:
CDS join(1..10,30..40,50..60)
Then the top level feature would be of type 'CDS' from 1 to 60 (actually 0
to 60 in Python counting) with location_operator='join', and the three sub-
features would also be of type 'CDS', and would be from 1 to 10, 30 to
40 and 50 to 60, respectively (although actually using Python counting).
To get the nucleotide sequence for this CDS, you would need to take the
parent sequence and do seq[0:10]+seq[29:40]+seq[49:60] (Python counting).
Things are more complicated with strands and fuzzy positions. To save you
dealing with all these special cases, the SeqFeature provides an extract
method to do this for you.
"""
def __init__(self, location = None, type = '', location_operator = '',
strand = None, id = "<unknown id>",
qualifiers = None, sub_features = None,
ref = None, ref_db = None):
"""Initialize a SeqFeature on a Sequence.
location can either be a FeatureLocation (with strand argument also
given if required), or None.
e.g. With no strand, on the forward strand, and on the reverse strand:
>>> from Bio.SeqFeature import SeqFeature, FeatureLocation
>>> f1 = SeqFeature(FeatureLocation(5, 10), type="domain")
>>> f1.strand == f1.location.strand == None
True
>>> f2 = SeqFeature(FeatureLocation(7, 110, strand=1), type="CDS")
>>> f2.strand == f2.location.strand == +1
True
>>> f3 = SeqFeature(FeatureLocation(9, 108, strand=-1), type="CDS")
>>> f3.strand == f3.location.strand == -1
True
An invalid strand will trigger an exception:
>>> f4 = SeqFeature(FeatureLocation(50, 60), strand=2)
Traceback (most recent call last):
...
ValueError: Strand should be +1, -1, 0 or None, not 2
Similarly if set via the FeatureLocation directly:
>>> loc4 = FeatureLocation(50, 60, strand=2)
Traceback (most recent call last):
...
ValueError: Strand should be +1, -1, 0 or None, not 2
For exact start/end positions, an integer can be used (as shown above)
as shorthand for the ExactPosition object. For non-exact locations, the
FeatureLocation must be specified via the appropriate position objects.
"""
if location is not None and not isinstance(location, FeatureLocation):
raise TypeError("FeatureLocation (or None) required for the location")
self.location = location
self.type = type
self.location_operator = location_operator
if strand is not None:
self.strand = strand
self.id = id
if qualifiers is None:
qualifiers = {}
self.qualifiers = qualifiers
if sub_features is None:
sub_features = []
self.sub_features = sub_features
if ref is not None:
self.ref = ref
if ref_db is not None:
self.ref_db = ref_db
def _get_strand(self):
return self.location.strand
def _set_strand(self, value):
try:
self.location.strand = value
except AttributeError:
if self.location is None:
if value is not None:
raise ValueError("Can't set strand without a location.")
else:
raise
strand = property(fget = _get_strand, fset = _set_strand,
doc = """Feature's strand
This is a shortcut for feature.location.strand
""")
def _get_ref(self):
return self.location.ref
def _set_ref(self, value):
try:
self.location.ref = value
except AttributeError:
if self.location is None:
if value is not None:
raise ValueError("Can't set ref without a location.")
else:
raise
ref = property(fget = _get_ref, fset = _set_ref,
doc = """Feature location reference (e.g. accession).
This is a shortcut for feature.location.ref
""")
def _get_ref_db(self):
return self.location.ref_db
def _set_ref_db(self, value):
self.location.ref_db = value
ref_db = property(fget = _get_ref_db, fset = _set_ref_db,
doc = """Feature location reference's database.
This is a shortcut for feature.location.ref_db
""")
def __repr__(self):
"""A string representation of the record for debugging."""
answer = "%s(%s" % (self.__class__.__name__, repr(self.location))
if self.type:
answer += ", type=%s" % repr(self.type)
if self.location_operator:
answer += ", location_operator=%s" % repr(self.location_operator)
if self.id and self.id != "<unknown id>":
answer += ", id=%s" % repr(self.id)
if self.ref:
answer += ", ref=%s" % repr(self.ref)
if self.ref_db:
answer += ", ref_db=%s" % repr(self.ref_db)
answer += ")"
return answer
def __str__(self):
"""A readable summary of the feature intended to be printed to screen.
"""
out = "type: %s\n" % self.type
out += "location: %s\n" % self.location
if self.id and self.id != "<unknown id>":
out += "id: %s\n" % self.id
out += "qualifiers: \n"
for qual_key in sorted(self.qualifiers):
out += " Key: %s, Value: %s\n" % (qual_key,
self.qualifiers[qual_key])
if len(self.sub_features) != 0:
out += "Sub-Features\n"
for sub_feature in self.sub_features:
out +="%s\n" % sub_feature
return out
def _shift(self, offset):
"""Returns a copy of the feature with its location shifted (PRIVATE).
The annotation qaulifiers are copied."""
return SeqFeature(location = self.location._shift(offset),
type = self.type,
location_operator = self.location_operator,
id = self.id,
qualifiers = dict(self.qualifiers.iteritems()),
sub_features = [f._shift(offset) for f in self.sub_features])
def _flip(self, length):
"""Returns a copy of the feature with its location flipped (PRIVATE).
The argument length gives the length of the parent sequence. For
example a location 0..20 (+1 strand) with parent length 30 becomes
after flipping 10..30 (-1 strand). Strandless (None) or unknown
strand (0) remain like that - just their end points are changed.
The annotation qaulifiers are copied.
"""
return SeqFeature(location = self.location._flip(length),
type = self.type,
location_operator = self.location_operator,
id = self.id,
qualifiers = dict(self.qualifiers.iteritems()),
sub_features = [f._flip(length) for f in self.sub_features[::-1]])
def extract(self, parent_sequence):
"""Extract feature sequence from the supplied parent sequence.
The parent_sequence can be a Seq like object or a string, and will
generally return an object of the same type. The exception to this is
a MutableSeq as the parent sequence will return a Seq object.
This should cope with complex locations including complements, joins
and fuzzy positions. Even mixed strand features should work! This
also covers features on protein sequences (e.g. domains), although
here reverse strand features are not permitted.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_protein
>>> from Bio.SeqFeature import SeqFeature, FeatureLocation
>>> seq = Seq("MKQHKAMIVALIVICITAVVAAL", generic_protein)
>>> f = SeqFeature(FeatureLocation(8,15), type="domain")
>>> f.extract(seq)
Seq('VALIVIC', ProteinAlphabet())
Note - currently only sub-features of type "join" are supported.
"""
if isinstance(parent_sequence, MutableSeq):
#This avoids complications with reverse complements
#(the MutableSeq reverse complement acts in situ)
parent_sequence = parent_sequence.toseq()
if self.sub_features:
if self.location_operator!="join":
raise ValueError(self.location_operator)
if self.location.strand == -1:
#This is a special case given how the GenBank parser works.
#Must avoid doing the reverse complement twice.
parts = []
for f_sub in self.sub_features[::-1]:
assert f_sub.location.strand==-1
parts.append(f_sub.location.extract(parent_sequence))
else:
#This copes with mixed strand features:
parts = [f_sub.location.extract(parent_sequence) \
for f_sub in self.sub_features]
#We use addition rather than a join to avoid alphabet issues:
f_seq = parts[0]
for part in parts[1:] : f_seq += part
return f_seq
else:
return self.location.extract(parent_sequence)
def __nonzero__(self):
"""Returns True regardless of the length of the feature.
This behaviour is for backwards compatibility, since until the
__len__ method was added, a SeqFeature always evaluated as True.
Note that in comparison, Seq objects, strings, lists, etc, will all
evaluate to False if they have length zero.
WARNING: The SeqFeature may in future evaluate to False when its
length is zero (in order to better match normal python behaviour)!
"""
return True
def __len__(self):
"""Returns the length of the region described by a feature.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_protein
>>> from Bio.SeqFeature import SeqFeature, FeatureLocation
>>> seq = Seq("MKQHKAMIVALIVICITAVVAAL", generic_protein)
>>> f = SeqFeature(FeatureLocation(8,15), type="domain")
>>> len(f)
7
>>> f.extract(seq)
Seq('VALIVIC', ProteinAlphabet())
>>> len(f.extract(seq))
7
For simple features without subfeatures this is the same as the region
spanned (end position minus start position). However, for a feature
defined by combining several subfeatures (e.g. a CDS as the join of
several exons) the gaps are not counted (e.g. introns). This ensures
that len(f) == len(f.extract(parent_seq)), and also makes sure things
work properly with features wrapping the origin etc.
"""
if self.sub_features:
return sum(len(f) for f in self.sub_features)
else:
return len(self.location)
def __iter__(self):
"""Iterate over the parent positions within the feature.
The iteration order is strand aware, and can be thought of as moving
along the feature using the parent sequence coordinates:
>>> from Bio.SeqFeature import SeqFeature, FeatureLocation
>>> f = SeqFeature(FeatureLocation(5,10), type="domain", strand=-1)
>>> len(f)
5
>>> for i in f: print i
9
8
7
6
5
>>> list(f)
[9, 8, 7, 6, 5]
"""
if self.sub_features:
if self.strand == -1:
for f in self.sub_features[::-1]:
for i in f.location:
yield i
else:
for f in self.sub_features:
for i in f.location:
yield i
else:
for i in self.location:
yield i
def __contains__(self, value):
"""Check if an integer position is within the feature.
>>> from Bio.SeqFeature import SeqFeature, FeatureLocation
>>> f = SeqFeature(FeatureLocation(5,10), type="domain", strand=-1)
>>> len(f)
5
>>> [i for i in range(15) if i in f]
[5, 6, 7, 8, 9]
For example, to see which features include a SNP position, you could
use this:
>>> from Bio import SeqIO
>>> record = SeqIO.read("GenBank/NC_000932.gb", "gb")
>>> for f in record.features:
... if 1750 in f:
... print f.type, f.location
source [0:154478](+)
gene [1716:4347](-)
tRNA [1716:4347](-)
Note that for a feature defined as a join of several subfeatures (e.g.
the union of several exons) the gaps are not checked (e.g. introns).
In this example, the tRNA location is defined in the GenBank file as
complement(join(1717..1751,4311..4347)), so that position 1760 falls
in the gap:
>>> for f in record.features:
... if 1760 in f:
... print f.type, f.location
source [0:154478](+)
gene [1716:4347](-)
Note that additional care may be required with fuzzy locations, for
example just before a BeforePosition:
>>> from Bio.SeqFeature import SeqFeature, FeatureLocation
>>> from Bio.SeqFeature import BeforePosition
>>> f = SeqFeature(FeatureLocation(BeforePosition(3),8), type="domain")
>>> len(f)
5
>>> [i for i in range(10) if i in f]
[3, 4, 5, 6, 7]
"""
if not isinstance(value, int):
raise ValueError("Currently we only support checking for integer "
"positions being within a SeqFeature.")
if self.sub_features:
for f in self.sub_features:
if value in f:
return True
return False
else:
return value in self.location
# --- References
# TODO -- Will this hold PubMed and Medline information decently?
class Reference(object):
"""Represent a Generic Reference object.
Attributes:
o location - A list of Location objects specifying regions of
the sequence that the references correspond to. If no locations are
specified, the entire sequence is assumed.
o authors - A big old string, or a list split by author, of authors
for the reference.
o title - The title of the reference.
o journal - Journal the reference was published in.
o medline_id - A medline reference for the article.
o pubmed_id - A pubmed reference for the article.
o comment - A place to stick any comments about the reference.
"""
def __init__(self):
self.location = []
self.authors = ''
self.consrtm = ''
self.title = ''
self.journal = ''
self.medline_id = ''
self.pubmed_id = ''
self.comment = ''
def __str__(self):
"""Output an informative string for debugging.
"""
out = ""
for single_location in self.location:
out += "location: %s\n" % single_location
out += "authors: %s\n" % self.authors
if self.consrtm:
out += "consrtm: %s\n" % self.consrtm
out += "title: %s\n" % self.title
out += "journal: %s\n" % self.journal
out += "medline id: %s\n" % self.medline_id
out += "pubmed id: %s\n" % self.pubmed_id
out += "comment: %s\n" % self.comment
return out
def __repr__(self):
#TODO - Update this is __init__ later accpets values
return "%s(title=%s, ...)" % (self.__class__.__name__,
repr(self.title))
# --- Handling feature locations
class FeatureLocation(object):
"""Specify the location of a feature along a sequence.
The FeatureLocation is used for simple continous features, which can
be described as running from a start position to and end position
(optionally with a strand and reference information). More complex
locations made up from several non-continuous parts (e.g. a coding
sequence made up of several exons) are described using multiple
FeatureLocation objects combined as a CompoundLocation object.
Note that the start and end location numbering follow Python's scheme,
thus a GenBank entry of 123..150 (one based counting) becomes a location
of [122:150] (zero based counting).
>>> from Bio.SeqFeature import FeatureLocation
>>> f = FeatureLocation(122, 150)
>>> print f
[122:150]
>>> print f.start
122
>>> print f.end
150
>>> print f.strand
None
Note the strand defaults to None. If you are working with nucleotide
sequences you'd want to be explicit if it is the forward strand:
>>> from Bio.SeqFeature import FeatureLocation
>>> f = FeatureLocation(122, 150, strand=+1)
>>> print f
[122:150](+)
>>> print f.strand
1
Note that for a parent sequence of length n, the FeatureLocation
start and end must satisfy the inequality 0 <= start <= end <= n.
This means even for features on the reverse strand of a nucleotide
sequence, we expect the 'start' coordindate to be less than the
'end' coordindate.
>>> from Bio.SeqFeature import FeatureLocation
>>> r = FeatureLocation(122, 150, strand=-1)
>>> print r
[122:150](-)
>>> print r.start
122
>>> print r.end
150
>>> print r.strand
-1
i.e. Rather than thinking of the 'start' and 'end' biologically in a
strand aware manor, think of them as the 'left most' or 'minimum'
boundary, and the 'right most' or 'maximum' boundary of the region
being described.
In the example above we have used standard exact positions, but there
are also specialised position objects used to represent fuzzy positions
as well, for example a GenBank location like complement(<123..150)
would use a BeforePosition object for the start.
"""
def __init__(self, start, end, strand=None, ref=None, ref_db=None):
"""Specify the start, end, strand etc of a sequence feature.
start and end arguments specify the values where the feature begins
and ends. These can either by any of the *Position objects that
inherit from AbstractPosition, or can just be integers specifying the
position. In the case of integers, the values are assumed to be
exact and are converted in ExactPosition arguments. This is meant
to make it easy to deal with non-fuzzy ends.
i.e. Short form:
>>> from Bio.SeqFeature import FeatureLocation
>>> loc = FeatureLocation(5, 10, strand=-1)
>>> print loc
[5:10](-)
Explicit form:
>>> from Bio.SeqFeature import FeatureLocation, ExactPosition
>>> loc = FeatureLocation(ExactPosition(5), ExactPosition(10), strand=-1)
>>> print loc
[5:10](-)
Other fuzzy positions are used similarly,
>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc2 = FeatureLocation(BeforePosition(5), AfterPosition(10), strand=-1)
>>> print loc2
[<5:>10](-)
For nucleotide features you will also want to specify the strand,
use 1 for the forward (plus) strand, -1 for the reverse (negative)
strand, 0 for stranded but strand unknown (? in GFF3), or None for
when the strand does not apply (dot in GFF3), e.g. features on
proteins.
>>> loc = FeatureLocation(5, 10, strand=+1)
>>> print loc
[5:10](+)
>>> print loc.strand
1
Normally feature locations are given relative to the parent
sequence you are working with, but an explicit accession can
be given with the optional ref and db_ref strings:
>>> loc = FeatureLocation(105172, 108462, ref="AL391218.9", strand=1)
>>> print loc
AL391218.9[105172:108462](+)
>>> print loc.ref
AL391218.9
"""
#TODO - Check 0 <= start <= end (<= length of reference)
if isinstance(start, AbstractPosition):
self._start = start
elif isinstance(start, int) or isinstance(start, long):
self._start = ExactPosition(start)
else:
raise TypeError("start=%r %s" % (start, type(start)))
if isinstance(end, AbstractPosition):
self._end = end
elif isinstance(end, int) or isinstance(end, long):
self._end = ExactPosition(end)
else:
raise TypeError("end=%r %s" % (end, type(end)))
self.strand = strand
self.ref = ref
self.ref_db = ref_db
def _get_strand(self):
return self._strand
def _set_strand(self, value):
if value not in [+1, -1, 0, None]:
raise ValueError("Strand should be +1, -1, 0 or None, not %r" \
% value)
self._strand = value
strand = property(fget = _get_strand, fset = _set_strand,
doc = "Strand of the location (+1, -1, 0 or None).")
def __str__(self):
"""Returns a representation of the location (with python counting).
For the simple case this uses the python splicing syntax, [122:150]
(zero based counting) which GenBank would call 123..150 (one based
counting).
"""
answer = "[%s:%s]" % (self._start, self._end)
if self.ref and self.ref_db:
answer = "%s:%s%s" % (self.ref_db, self.ref, answer)
elif self.ref:
answer = self.ref + answer
#Is ref_db without ref meaningful?
if self.strand is None:
return answer
elif self.strand == +1:
return answer + "(+)"
elif self.strand == -1:
return answer + "(-)"
else:
#strand = 0, stranded but strand unknown, ? in GFF3
return answer + "(?)"
def __repr__(self):
"""A string representation of the location for debugging."""
optional = ""
if self.strand is not None:
optional += ", strand=%r" % self.strand
if self.ref is not None:
optional += ", ref=%r" % self.ref
if self.ref_db is not None:
optional += ", ref_db=%r" % self.ref_db
return "%s(%r, %r%s)" \
% (self.__class__.__name__, self.start, self.end, optional)
def __nonzero__(self):
"""Returns True regardless of the length of the feature.
This behaviour is for backwards compatibility, since until the
__len__ method was added, a FeatureLocation always evaluated as True.
Note that in comparison, Seq objects, strings, lists, etc, will all
evaluate to False if they have length zero.
WARNING: The FeatureLocation may in future evaluate to False when its
length is zero (in order to better match normal python behaviour)!
"""
return True
def __len__(self):
"""Returns the length of the region described by the FeatureLocation.
Note that extra care may be needed for fuzzy locations, e.g.
>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10))
>>> len(loc)
5
"""
return int(self._end) - int(self._start)
def __contains__(self, value):
"""Check if an integer position is within the FeatureLocation.
Note that extra care may be needed for fuzzy locations, e.g.
>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10))
>>> len(loc)
5
>>> [i for i in range(15) if i in loc]
[5, 6, 7, 8, 9]
"""
if not isinstance(value, int):
raise ValueError("Currently we only support checking for integer "
"positions being within a FeatureLocation.")
if value < self._start or value >= self._end:
return False
else:
return True
def __iter__(self):
"""Iterate over the parent positions within the FeatureLocation.
>>> from Bio.SeqFeature import FeatureLocation
>>> from Bio.SeqFeature import BeforePosition, AfterPosition
>>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10))
>>> len(loc)
5
>>> for i in loc: print i
5
6
7
8
9
>>> list(loc)
[5, 6, 7, 8, 9]
>>> [i for i in range(15) if i in loc]
[5, 6, 7, 8, 9]
Note this is strand aware:
>>> loc = FeatureLocation(BeforePosition(5), AfterPosition(10), strand = -1)
>>> list(loc)
[9, 8, 7, 6, 5]
"""
if self.strand == -1:
for i in range(self._end - 1, self._start - 1, -1):
yield i
else:
for i in range(self._start, self._end):
yield i
def _shift(self, offset):
"""Returns a copy of the location shifted by the offset (PRIVATE)."""
if self.ref or self.ref_db:
#TODO - Return self?
raise ValueError("Feature references another sequence.")
return FeatureLocation(start = self._start._shift(offset),
end = self._end._shift(offset),
strand = self.strand)
def _flip(self, length):
"""Returns a copy of the location after the parent is reversed (PRIVATE)."""
if self.ref or self.ref_db:
#TODO - Return self?
raise ValueError("Feature references another sequence.")
#Note this will flip the start and end too!
if self.strand == +1:
flip_strand = -1
elif self.strand == -1:
flip_strand = +1
else:
#0 or None
flip_strand = self.strand
return FeatureLocation(start = self._end._flip(length),
end = self._start._flip(length),
strand = flip_strand)
@property
def start(self):
"""Start location (integer like, possibly a fuzzy position, read only)."""
return self._start
@property
def end(self):
"""End location (integer like, possibly a fuzzy position, read only)."""
return self._end
@property
def nofuzzy_start(self):
"""Start position (integer, approximated if fuzzy, read only) (OBSOLETE).
This is now a alias for int(feature.start), which should be
used in preference -- unless you are trying to support old
versions of Biopython.
"""
return int(self._start)
@property
def nofuzzy_end(self):
"""End position (integer, approximated if fuzzy, read only) (OBSOLETE).
This is now a alias for int(feature.end), which should be
used in preference -- unless you are trying to support old
versions of Biopython.
"""
return int(self._end)
def extract(self, parent_sequence):
"""Extract feature sequence from the supplied parent sequence."""
if self.ref or self.ref_db:
#TODO - Take a dictionary as an optional argument?
raise ValueError("Feature references another sequence.")
if isinstance(parent_sequence, MutableSeq):
#This avoids complications with reverse complements
#(the MutableSeq reverse complement acts in situ)
parent_sequence = parent_sequence.toseq()
f_seq = parent_sequence[self.nofuzzy_start:self.nofuzzy_end]
if self.strand == -1:
try:
f_seq = f_seq.reverse_complement()
except AttributeError:
assert isinstance(f_seq, str)
f_seq = reverse_complement(f_seq)
return f_seq
class AbstractPosition(object):
"""Abstract base class representing a position.
"""
def __repr__(self):
"""String representation of the location for debugging."""
return "%s(...)" % (self.__class__.__name__)
class ExactPosition(int, AbstractPosition):
"""Specify the specific position of a boundary.
o position - The position of the boundary.
o extension - An optional argument which must be zero since we don't
have an extension. The argument is provided so that the same number of
arguments can be passed to all position types.
In this case, there is no fuzziness associated with the position.
>>> p = ExactPosition(5)
>>> p
ExactPosition(5)
>>> print p
5
>>> isinstance(p, AbstractPosition)
True
>>> isinstance(p, int)
True
Integer comparisons and operations should work as expected:
>>> p == 5
True
>>> p < 6
True
>>> p <= 5
True
>>> p + 10
15
"""
def __new__(cls, position, extension = 0):
if extension != 0:
raise AttributeError("Non-zero extension %s for exact position."
% extension)
return int.__new__(cls, position)
def __repr__(self):
"""String representation of the ExactPosition location for debugging."""
return "%s(%i)" % (self.__class__.__name__, int(self))
@property
def position(self):
"""Legacy attribute to get position as integer (OBSOLETE)."""
return int(self)
@property
def extension(self):
"""Legacy attribute to get extension (zero) as integer (OBSOLETE)."""
return 0
def _shift(self, offset):
#By default preserve any subclass
return self.__class__(int(self) + offset)
def _flip(self, length):
#By default perserve any subclass
return self.__class__(length - int(self))
class UncertainPosition(ExactPosition):
"""Specify a specific position which is uncertain.
This is used in UniProt, e.g. ?222 for uncertain position 222, or in the
XML format explicitly marked as uncertain. Does not apply to GenBank/EMBL.
"""
pass
class UnknownPosition(AbstractPosition):
"""Specify a specific position which is unknown (has no position).
This is used in UniProt, e.g. ? or in the XML as unknown.
"""
def __repr__(self):
"""String representation of the UnknownPosition location for debugging."""
return "%s()" % self.__class__.__name__
def __hash__(self):
return hash(None)
@property
def position(self):
"""Legacy attribute to get position (None) (OBSOLETE)."""
return None
@property
def extension(self):
"""Legacy attribute to get extension (zero) as integer (OBSOLETE)."""
return 0
def _shift(self, offset):
return self
def _flip(self, length):
return self
class WithinPosition(int, AbstractPosition):
"""Specify the position of a boundary within some coordinates.
Arguments:
o position - The default integer position
o left - The start (left) position of the boundary
o right - The end (right) position of the boundary
This allows dealing with a position like ((1.4)..100). This
indicates that the start of the sequence is somewhere between 1
and 4. Since this is a start coordindate, it should acts like
it is at position 1 (or in Python counting, 0).
>>> p = WithinPosition(10,10,13)
>>> p
WithinPosition(10, left=10, right=13)
>>> print p
(10.13)
>>> int(p)
10
Basic integer comparisons and operations should work as though
this were a plain integer:
>>> p == 10
True
>>> p in [9,10,11]
True
>>> p < 11
True
>>> p + 10
20
>>> isinstance(p, WithinPosition)
True
>>> isinstance(p, AbstractPosition)
True
>>> isinstance(p, int)
True
Note this also applies for comparison to other position objects,
where again the integer behaviour is used:
>>> p == 10
True
>>> p == ExactPosition(10)
True
>>> p == BeforePosition(10)
True
>>> p == AfterPosition(10)
True
If this were an end point, you would want the position to be 13:
>>> p2 = WithinPosition(13,10,13)
>>> p2
WithinPosition(13, left=10, right=13)
>>> print p2
(10.13)
>>> int(p2)
13
>>> p2 == 13
True
>>> p2 == ExactPosition(13)
True
The old legacy properties of position and extension give the
starting/lower/left position as an integer, and the distance
to the ending/higher/right position as an integer. Note that
the position object will act like either the left or the right
end-point depending on how it was created:
>>> p.position == p2.position == 10
True
>>> p.extension == p2.extension == 3
True
>>> int(p) == int(p2)
False
>>> p == 10
True
>>> p2 == 13
True
"""
def __new__(cls, position, left, right):
assert position==left or position==right, \
"WithinPosition: %r should match left %r or right %r" \
(position, left, right)
obj = int.__new__(cls, position)
obj._left = left
obj._right = right
return obj
def __repr__(self):
"""String representation of the WithinPosition location for debugging."""
return "%s(%i, left=%i, right=%i)" \
% (self.__class__.__name__, int(self),
self._left, self._right)
def __str__(self):
return "(%s.%s)" % (self._left, self._right)
@property
def position(self):
"""Legacy attribute to get (left) position as integer (OBSOLETE)."""
return self._left
@property
def extension(self):
"""Legacy attribute to get extension (from left to right) as an integer (OBSOLETE)."""
return self._right - self._left
def _shift(self, offset):
return self.__class__(int(self) + offset,
self._left + offset,
self._right + offset)
def _flip(self, length):
return self.__class__(length - int(self),
length - self._right,
length - self._left)
class BetweenPosition(int, AbstractPosition):
"""Specify the position of a boundary between two coordinates (OBSOLETE?).
Arguments:
o position - The default integer position
o left - The start (left) position of the boundary
o right - The end (right) position of the boundary
This allows dealing with a position like 123^456. This
indicates that the start of the sequence is somewhere between
123 and 456. It is up to the parser to set the position argument
to either boundary point (depending on if this is being used as
a start or end of the feature). For example as a feature end:
>>> p = BetweenPosition(456, 123, 456)
>>> p
BetweenPosition(456, left=123, right=456)
>>> print p
(123^456)
>>> int(p)
456
Integer equality and comparison use the given position,
>>> p == 456
True
>>> p in [455, 456, 457]
True
>>> p > 300
True
The old legacy properties of position and extension give the
starting/lower/left position as an integer, and the distance
to the ending/higher/right position as an integer. Note that
the position object will act like either the left or the right
end-point depending on how it was created:
>>> p2 = BetweenPosition(123, left=123, right=456)
>>> p.position == p2.position == 123
True
>>> p.extension
333
>>> p2.extension
333
>>> p.extension == p2.extension == 333
True
>>> int(p) == int(p2)
False
>>> p == 456
True
>>> p2 == 123
True
Note this potentially surprising behaviour:
>>> BetweenPosition(123, left=123, right=456) == ExactPosition(123)
True
>>> BetweenPosition(123, left=123, right=456) == BeforePosition(123)
True
>>> BetweenPosition(123, left=123, right=456) == AfterPosition(123)
True
i.e. For equality (and sorting) the position objects behave like
integers.
"""
def __new__(cls, position, left, right):
assert position==left or position==right
obj = int.__new__(cls, position)
obj._left = left
obj._right = right
return obj
def __repr__(self):
"""String representation of the WithinPosition location for debugging."""
return "%s(%i, left=%i, right=%i)" \
% (self.__class__.__name__, int(self),
self._left, self._right)
def __str__(self):
return "(%s^%s)" % (self._left, self._right)
@property
def position(self):
"""Legacy attribute to get (left) position as integer (OBSOLETE)."""
return self._left
@property
def extension(self):
"""Legacy attribute to get extension (from left to right) as an integer (OBSOLETE)."""
return self._right - self._left
def _shift(self, offset):
return self.__class__(int(self) + offset,
self._left + offset,
self._right + offset)
def _flip(self, length):
return self.__class__(length - int(self),
length - self._right,
length - self._left)
class BeforePosition(int, AbstractPosition):
"""Specify a position where the actual location occurs before it.
Arguments:
o position - The upper boundary of where the location can occur.
o extension - An optional argument which must be zero since we don't
have an extension. The argument is provided so that the same number of
arguments can be passed to all position types.
This is used to specify positions like (<10..100) where the location
occurs somewhere before position 10.
>>> p = BeforePosition(5)
>>> p
BeforePosition(5)
>>> print p
<5
>>> int(p)
5
>>> p + 10
15
Note this potentially surprising behaviour:
>>> p == ExactPosition(5)
True
>>> p == AfterPosition(5)
True
Just remember that for equality and sorting the position objects act
like integers.
"""
#Subclasses int so can't use __init__
def __new__(cls, position, extension = 0):
if extension != 0:
raise AttributeError("Non-zero extension %s for exact position."
% extension)
return int.__new__(cls, position)
@property
def position(self):
"""Legacy attribute to get position as integer (OBSOLETE)."""
return int(self)
@property
def extension(self):
"""Legacy attribute to get extension (zero) as integer (OBSOLETE)."""
return 0
def __repr__(self):
"""A string representation of the location for debugging."""
return "%s(%i)" % (self.__class__.__name__, int(self))
def __str__(self):
return "<%s" % self.position
def _shift(self, offset):
return self.__class__(int(self) + offset)
def _flip(self, length):
return AfterPosition(length - int(self))
class AfterPosition(int, AbstractPosition):
"""Specify a position where the actual location is found after it.
Arguments:
o position - The lower boundary of where the location can occur.
o extension - An optional argument which must be zero since we don't
have an extension. The argument is provided so that the same number of
arguments can be passed to all position types.
This is used to specify positions like (>10..100) where the location
occurs somewhere after position 10.
>>> p = AfterPosition(7)
>>> p
AfterPosition(7)
>>> print p
>7
>>> int(p)
7
>>> p + 10
17
>>> isinstance(p, AfterPosition)
True
>>> isinstance(p, AbstractPosition)
True
>>> isinstance(p, int)
True
Note this potentially surprising behaviour:
>>> p == ExactPosition(7)
True
>>> p == BeforePosition(7)
True
Just remember that for equality and sorting the position objects act
like integers.
"""
#Subclasses int so can't use __init__
def __new__(cls, position, extension = 0):
if extension != 0:
raise AttributeError("Non-zero extension %s for exact position."
% extension)
return int.__new__(cls, position)
@property
def position(self):
"""Legacy attribute to get position as integer (OBSOLETE)."""
return int(self)
@property
def extension(self):
"""Legacy attribute to get extension (zero) as integer (OBSOLETE)."""
return 0
def __repr__(self):
"""A string representation of the location for debugging."""
return "%s(%i)" % (self.__class__.__name__, int(self))
def __str__(self):
return ">%s" % self.position
def _shift(self, offset):
return self.__class__(int(self) + offset)
def _flip(self, length):
return BeforePosition(length - int(self))
class OneOfPosition(int, AbstractPosition):
"""Specify a position where the location can be multiple positions.
This models the GenBank 'one-of(1888,1901)' function, and tries
to make this fit within the Biopython Position models. If this was
a start position it should act like 1888, but as an end position 1901.
>>> p = OneOfPosition(1888, [ExactPosition(1888), ExactPosition(1901)])
>>> p
OneOfPosition(1888, choices=[ExactPosition(1888), ExactPosition(1901)])
>>> int(p)
1888
Interget comparisons and operators act like using int(p),
>>> p == 1888
True
>>> p <= 1888
True
>>> p > 1888
False
>>> p + 100
1988
>>> isinstance(p, OneOfPosition)
True
>>> isinstance(p, AbstractPosition)
True
>>> isinstance(p, int)
True
The old legacy properties of position and extension give the
starting/lowest/left-most position as an integer, and the
distance to the ending/highest/right-most position as an integer.
Note that the position object will act like one of the list of
possible locations depending on how it was created:
>>> p2 = OneOfPosition(1901, [ExactPosition(1888), ExactPosition(1901)])
>>> p.position == p2.position == 1888
True
>>> p.extension == p2.extension == 13
True
>>> int(p) == int(p2)
False
>>> p == 1888
True
>>> p2 == 1901
True
"""
def __new__(cls, position, choices):
"""Initialize with a set of posssible positions.
position_list is a list of AbstractPosition derived objects,
specifying possible locations.
position is an integer specifying the default behaviour.
"""
assert position in choices, \
"OneOfPosition: %r should match one of %r" % (position, choices)
obj = int.__new__(cls, position)
obj.position_choices = choices
return obj
@property
def position(self):
"""Legacy attribute to get (left) position as integer (OBSOLETE)."""
return min(int(pos) for pos in self.position_choices)
@property
def extension(self):
"""Legacy attribute to get extension as integer (OBSOLETE)."""
positions = [int(pos) for pos in self.position_choices]
return max(positions) - min(positions)
def __repr__(self):
"""String representation of the OneOfPosition location for debugging."""
return "%s(%i, choices=%r)" % (self.__class__.__name__, \
int(self), self.position_choices)
def __str__(self):
out = "one-of("
for position in self.position_choices:
out += "%s," % position
# replace the last comma with the closing parenthesis
out = out[:-1] + ")"
return out
def _shift(self, offset):
return self.__class__(int(self) + offset,
[p._shift(offset) for p in self.position_choices])
def _flip(self, length):
return self.__class__(length - int(self),
[p._flip(length) for p in self.position_choices[::-1]])
class PositionGap(object):
"""Simple class to hold information about a gap between positions.
"""
def __init__(self, gap_size):
"""Intialize with a position object containing the gap information.
"""
self.gap_size = gap_size
def __repr__(self):
"""A string representation of the position gap for debugging."""
return "%s(%s)" % (self.__class__.__name__, repr(self.gap_size))
def __str__(self):
out = "gap(%s)" % self.gap_size
return out
def _test():
"""Run the Bio.SeqFeature module's doctests (PRIVATE).
This will try and locate the unit tests directory, and run the doctests
from there in order that the relative paths used in the examples work.
"""
import doctest
import os
if os.path.isdir(os.path.join("..","Tests")):
print "Runing doctests..."
cur_dir = os.path.abspath(os.curdir)
os.chdir(os.path.join("..","Tests"))
doctest.testmod()
os.chdir(cur_dir)
del cur_dir
print "Done"
elif os.path.isdir(os.path.join("Tests")) :
print "Runing doctests..."
cur_dir = os.path.abspath(os.curdir)
os.chdir(os.path.join("Tests"))
doctest.testmod()
os.chdir(cur_dir)
del cur_dir
print "Done"
if __name__ == "__main__":
_test()
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